The formation of bonding pad protective layer over exposed bonding pad materials between stacked integrated circuit (IC) dies or wafers is described in preferred embodiments in which the bonding pad protective layer is formed in the integrated process of forming wafer bonding pads. The bonding pad protective layer prevents the exposed bonding pad materials from oxidation and corrosion in open-air or other harsh environments. By providing a bonding pad protective layer on exposed bonding pad materials, significant product reliability improvement is expected on ICs having a three-dimensional “stacked-die” configuration.